Department of Genetics, Stanford University, Palo Alto, California 94305-5120 (USA)
emmadann@stanford.edu | emdann.github.io | emdann
Education
PhD in Biological Sciences – University of Cambridge, UK (Oct 2019 – Oct 2023)
Advisors: Dr. Sarah A. Teichmann, Dr. John C. Marioni
Thesis title: Discovering variation from cell atlases: comparative methods for single-cell genomics
M.Sc. in Cancer, Stem Cells and Developmental Biology (Bioinformatics profile) – Utrecht University, NL (Sept 2017 – Aug 2019)
Final grade: cum laude (Honours, Avg. grade: 9.10/10)
B.Sc. in Biomolecular Sciences and Technology – University of Trento, IT (Sept 2014 – July 2017)
Final grade: 110 cum laude/110 (Avg. grade: 29.58/30)
Professional experience
Post-doctoral fellow – Stanford University, Palo Alto, USA (May 2024 – present)
Hosted by Jonathan Pritchard and Alex Marson (visiting fellow at Gladstone Institute for Genomic Immunology)
Core team member – scverse consortium (Feb 2024 – present)
Community and teaching
Data science consultant – Ensocell Ltd (Oct 2023 – Mar 2024)
Target discovery platform and analysis of single-cell data
Graduate researcher – Wellcome Sanger Institute, Cambridge, UK (Oct 2019 – Jan 2024)
Supervised by Sarah Teichmann and John Marioni. Statistical methods for comparative analysis of single-cell omics data.
Research intern – European Molecular Biology Laboratory, Heidelberg, DE (Sept 2018 – Aug 2019)
Supervised by Wolfgang Huber. Integrative analysis of multi-omic profiles of perturbations for functional characterization of drug treatments and target discovery.
Research intern – KNAW Hubrecht Institute, Utrecht, NL (Sept 2017 – Aug 2018)
Supervised by Alexander Van Ourdenaarden. Biophysical modelling of whole-genome amplification via random priming, to predict and enhance coverage of single-cell bisulfite sequencing experiments.
Research intern – Center for Integrative Biology, University of Trento, IT (Feb 2017 – July 2017)
Supervised by Francesca Demichelis. Computational analysis of whole-methylome profiles of tumor samples from a large cohort of prostate cancer patients, for epigenetic biomarker discovery.
Research assistant – Center for Integrative Biology, University of Trento, IT (Feb 2016 – Feb 2017)
Lab equipment maintenance and general support for benchwork.
Publications
(*) denotes equal contribution as co-first author
Journal articles
Missarova A., Dann E., … , J.C. Marioni (2023) Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE. Genome Biology | Full text | R package
Barnes J. L., He P., … , Dann E., … , Teichmann S.A., Meyer K. B., Nikolic M. Z. (2022) Early human lung immune cell development and its role in epithelial cell fate. Science Immunology | Full text
Dann E., Cujba A.M., Oliver A., Meyer K., Teichmann S.A., Marioni J.C. (2023) Precise identification of cell states altered in disease with healthy single-cell references, Nature Genetics | Full text | code | python package
Botting R.A., Goh I., … , Dann E., … , Teichmann S.A. , Haniffa M. (2023) Yolk sac cell atlas reveals multiorgan functions during human early development. Science | Full text
Suo C., Polanski K., Dann E., … , Tuong Z.K., Clatworthy M., Teichmann S.A. (2023) Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins, Nature Biotechnology | Full text | python package
Heumos L., … Single-cell Best Practices Consortium, … , Theis F.J. (2023) Best practices for single-cell analysis across modalities. Nature Review Genetics | Full text
Suo C.*, Dann E.*, … , Haniffa M., Teichmann S.A. (2022) Mapping the developing human immune system across organs. Science | Full text | code | data
He P., Lim K., Sun D., … , Dann E., … , Meyer K.B., Rawlins E.L. (2022) A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates, Cell | Full text
Kleshchevnikov V., Shmatko A., Dann E., …, Stegle O., Bayraktar O.A. (2022) Cell2location maps fine-grained cell types in spatial transcriptomics. Nature Biotechnology | Full text | python package
Dann E., Henderson N.C., Teichmann S.A., Morgan M.D., Marioni J.C. (2022) Differential abundance testing on single-cell data using k-nearest neighbor graphs, Nature Biotechnology | Full text | R package | python package
Jardine L., Webb S., … , Dann E., … , Göttgens B., Roberts I., Teichmann S. and Haniffa M. (2021) Blood and immune development in human fetal bone marrow and Down syndrome, Nature | Full text
Elmentaite R., Kumasaka N., Roberts K., Fleming A., Dann E., … , James K.R., Teichmann S.A. (2021), Cells of the human intestinal tract mapped across space and time, Nature | Full text
Stephenson E., Reynolds G., Botting R.A., Calero-Nieto F.J., Morgan M.D., Tuong Z.K., Bach K., Sungnak W., … , Dann E., … , Duncan C.J.A, Smith K., Teichmann S.A., Clatworthy M.R., Marioni J.C., Gottgens B., Haniffa M. (2020) Single-cell multi-omics analysis of the immune response in COVID-19, Nature Medicine | Full text
Beltran H., Romanel A., … , Dann E., … , Benelli M., and Demichelis F. (2020) Circulating Tumor DNA Profile Recognizes Transformation to Castration-Resistant Neuroendocrine Prostate Cancer, Journal of Clinical Investigation | Full text
Conference papers
Lalchand V.*, Ravuri A.*, Dann E.*, … , Teichmann S.A., Lawrence N.D. (2022) Modelling Technical and Biological Effects in scRNA-seq data with Scalable GPLVMs. Proceedings of the 17th Machine Learning in Computational Biology meeting | Full text
Pre-prints
Oliver A.J., Ni H., … , Dann E., …, Elmentaite R., Teichmann S.A. (2024) Single Cell Integration Characterises Gastric Cell Metaplasia in Inflammatory Intestinal Diseases. biorXiv (accepted at Nature) | Full text
Heumos L., Ji Y., … , Dann E., …, Theis F.J. (2024) Pertpy: an end-to-end framework for perturbation analysis. biorXiv | Full text | python package
Dann E.*, Teeple E.*, Elmentaite R., Meyer K., Gaglia G., Nestle F., Savova V., Rinaldis E., Teichmann S.A. (2024) Estimating the impact of single-cell RNA sequencing of
human tissues on drug target validation., medRxiv | Full text |
code
*Equal Contribution
Luecken M., Gigante S., Burkhardt D., Cannoodt R., … , Dann E., … , Saeys Y., Theis F.J., Krishnaswamy S. (2024) Defining and benchmarking open problems in single-cell analysis. | Full text
Yayon N., Kedlian V., … , Dann E., … , Teichmann S.A. (2023) A spatial human thymus cell atlas mapped to a continuous tissue axis. biorXiv | Full text
Schuster V., Dann E., Krogh A., Teichmann S.A. (2023) multiDGD: A versatile deep generative model for multi-omics data. biorXiv | Full text | python package
Sumanaweera D., Suo C., Muraro D., Dann E., … , Teichmann S.A. (2023) Gene-level alignment of single cell trajectories informs the progression of in vitro T cell differentiation. biorXiv | Full text | python package
Software
miloR | MarioniLab/miloR | primary developer | R/Bioconductor package for the identification of differential cell abundance in KNN graphs for single-cell data
milopy | emdann/milopy | primary developer | python package for the identification of differential cell abundance in KNN graphs for single-cell data
oor_benchmark | MarioniLab/oor_benchmark | primary developer | python framework to benchmark workflows for detection of out-of-reference cells in comparative single-cell analysis
genomic-features | scverse/genomic-features | primary developer | Genomic annotations using Bioconductor resources in Python.
pertpy | scverse/pertpy | contributor | perturbation analysis toolkit for the scverse ecosystem.
scverse-tutorials | scverse/scverse-tutorials | contributor | tutorials for single-cell omics data analysis in python
single-cell-best-practices | theislab/single-cell-best-practices | contributor | open source book on best practices for single-cell genomics data analysis
cell2location | BayraktarLab/cell2location | contributor | python package for mapping of tissue cell types via integration of single cell RNA-seq and spatial transcriptomics data
Presentations
Conference oral presentations
Nov 2022 - Machine Learning in Computational Biology conference, virtual
June 2022 - Single Cell Biology conference, Wellcome Genome Campus, Hinxton (UK)
May 2022 - The Biology of Genomes, Cold Spring Harbor Laboratory (US)
Oct 2021 - Chan Zuckerberg Initiative Single Cell Biology Meeting, virtual
Sept 2021 - Next Generation Genomics Meeting, virtual
Mar 2021 - CZI Seed Networks Computational biology meeting, virtual
Invited seminars
Sept 2024 - BRAID Genentech, South San Francisco (US)
Sept 2024 - Human Genetics department, University of Chicago, Chicago (US)
Sept 2024 - SQLIFTS Lecture Series, Northwestern University, Chicago (US)
Mar 2024 - Human Technopole, Milan (IT)
Dec 2023 - Google DeepMind, London (UK)
Aug 2023 - University of Sri Jayewardenepura single-cell genomics seminar series, virtual
Jul 2023 - Sanofi Precision Medicine & Computational biology, Cambridge (US)
Jun 2023 - Chan Zuckerberg Initiative, Redwood City (US)
Apr 2023 - Cambridge AI club for biomedicine, Milner Institute, Cambridge (UK)
Dec 2022 - UMC Utrecht single-cell genomics meeting, virtual
Sept 2022 - UK Conference of Bioinformatics and Computational Biology, virtual
Jul 2022 - Computational Health Center seminar, Helmholtz Munich (DE)
Apr 2022 - Maxwell Society Annual Conference, King’s College London (UK)
Apr 2022 - NYU Langone single cell journal club, virtual
Mar 2021 - Cambridge Center for Physical Biology Single Cell Symposium, virtual
Conference poster presentations
July 2023 - Human Cell Atlas General Meeting, Toronto (CA)
Oct 2022 - Single Cell Genomics conference, Utrecht (NL)
Jun 2021 - Human Cell Atlas General Meeting, virtual
Other meetings and events
Apr 2023 - Scverse community hackathon on software interoperability, Heidelberg (DE)
Dec 2022 - Scverse community hackathon on documentation, Innsbruck (AT)
Apr 2021 - Open Problems in Single-Cell Analysis Jamboree, virtual
Fellowships & awards
Nov 2024 - Helen Hay Whitney post-doctoral fellowship
Jul 2024 - EMBO long-term post-doctoral fellowship
Oct 2019 - Wellcome Sanger Institute PhD studentship (Wellcome Trust, UK)
Jan 2018 - U/Select honours programme and travel grant (Utrecht University, NL)
Oct 2017 - Merit Award for excellent graduates (University of Trento, IT)
Teaching & mentoring experience
Mar 2023 - Introduction to multiomics data integration and visualisation (EMBL-EBI training course) – Instructor for data integration case study
Jul 2022 - Systems biology: From large datasets to biological insight (EMBL-EBI training course) – Instructor for single-cell multi-omics module
Apr 2022 - Advanced topics in Single Cell Genomics (Swiss Institute for Bioinformatics course) – Trainer for multi-omics module
Aug 2021 - Advanced topics in Single Cell Genomics (SciLifeLab / Swiss Institute for Bioinformatics Summer School) – Trainer for multi-omics project
Fall 2021 - PhD rotation student recruitment and mentoring, Teichmann lab
Professional service
Conference/workshop organization
Sept 2024 - Scverse conference, Munich (DE) - co-organizer
Nov 2023 - Scverse hackathon on multi-condition analysis tools, Cambridge (UK) - main organizer
Fall 2023 - Open Problems Single-cell perturbations Kaggle competition - member of judge panel
Apr 2021 - Open Problems in Single-Cell Analysis Jamboree - co-organizer
Feb 2020 - EBI-Sanger-Cambridge PhD Symposium - member of the organizing committee
Outreach
Sanger prize competition - member of the selection panel (Mar 2023)
The Sanger Prize competition funds research internships at Sanger for undergraduate students from LMI countries. I’ve volunteered as a member of the Grad Panel, evaluating essays from applicants.
Open Wet Lab (OWL) - board member (Oct 2015 – Jan 2018)
OWL is the first biohacking organization in Italy. I was in charge of the association’s budget and directed the publication of OWL’s blog and scientific outreach articles for local newspapers.
Peer review
Nature (1 paper)
Nature Biotechnology (2* papers)
Cell (1* paper)
OUP Bioinformatics (1 paper)
Bioinformatics Advances (1 paper)
Machine Learning in Computational Biology (MLCB)
*Assisting a senior reviewer